├── .gitignore ├── INSTALL.md ├── LICENSE ├── README.md ├── blackbox ├── copy_lammps_results.sh ├── ibi.sh ├── pmf.sh ├── prepare_lammps_config.sh └── prepare_lammps_config_pmf.sh ├── config_files ├── bac_example │ ├── analysis_scripts │ │ └── .keep │ ├── build │ │ ├── complex.crd │ │ ├── complex.pdb │ │ └── complex.top │ ├── constraint │ │ └── .keep │ ├── data │ │ └── .keep │ ├── dcds │ │ └── .keep │ ├── equilibration │ │ └── .keep │ ├── fe-calc │ │ ├── amber_traj │ │ │ └── .keep │ │ └── build │ │ │ ├── com.crd │ │ │ ├── com.pdb │ │ │ ├── com.top │ │ │ ├── lig.crd │ │ │ ├── lig.pdb │ │ │ ├── lig.top │ │ │ ├── rec.crd │ │ │ ├── rec.pdb │ │ │ └── rec.top │ ├── mineq_confs │ │ ├── eq0.conf │ │ ├── eq1.conf │ │ └── eq2.conf │ ├── run_scripts │ │ └── .keep │ ├── sim_confs │ │ └── sim1.conf │ └── simulation │ │ └── .keep ├── ibi_example_poly1 │ ├── angle.1.extrap.end │ ├── bond.3.new.1 │ ├── in.CG.lammps │ ├── interaction_list │ ├── lammps_data_file │ ├── pot.1.1 │ ├── pot.1.new.1.1 │ └── rdf.1.1 ├── lammps_lj_liquid │ ├── INFO │ └── in.CG.lammps └── namd_toy_model │ ├── build │ ├── leap.log │ ├── mol-solv.crd │ ├── mol-solv.pdb │ ├── mol-solv.top │ ├── pep.pdb │ ├── tleap.in │ └── tleap.log │ └── sim_confs │ ├── eq.conf │ └── sim.conf ├── deploy ├── .jobscripts │ └── test.sh ├── BioMD │ ├── __init__.py │ ├── fabBioMD.py │ └── templates │ │ ├── bac-archer │ │ ├── bac-archer-nm-remote │ │ ├── bac-archer-nmode │ │ ├── bac-esmacs-whole-namd-supermuc │ │ ├── bac-esmacs-whole-nmode-supermuc │ │ ├── bac-supermuc │ │ ├── bac-ties-archer │ │ ├── bac-ties-archer-v2 │ │ ├── bac-ties-supermuc │ │ ├── bac-wonder-namd │ │ ├── bac-wonder1-nm-remote │ │ ├── bac-wonder1-nmode │ │ ├── bac-wonder1-nmode-test │ │ ├── bac-wonder2-nm-remote │ │ ├── bac-wonder2-nmode │ │ ├── bac-wonder2-nmode-test │ │ ├── fep.tcl │ │ ├── namd │ │ └── nmode.in ├── NanoMD │ ├── __init__.py │ └── fabNanoMD.py ├── __init__.py ├── data_proc │ ├── __init__.py │ ├── data.py │ └── dataNanoMD.py ├── fab.py ├── lammps-systems.yml ├── machines.py ├── machines.yml ├── machines_user_example.yml ├── templates.py ├── templates │ ├── lammps │ ├── ll │ ├── ll-supermuc │ ├── lsf1 │ ├── lsf2 │ ├── no_batch │ ├── pbs │ ├── pbs-archer │ ├── redis_header.txt │ └── sge └── test_data │ └── test_plot.txt ├── doc ├── FabBioMD-examples.md ├── FabNanoMD-examples.md └── commands-list.txt ├── fabfile.py └── python ├── IBI.py ├── IBI.py.requirements ├── PMF.py ├── filter_pot.py ├── lib ├── .hgignore ├── DataAnalysis.py ├── DataMorphing.py ├── LammpsIO.py ├── LammpsOutputAnalysis.py └── __init__.py └── plot_lammps.py /.gitignore: -------------------------------------------------------------------------------- 1 | deploy/machines_user.yml 2 | -------------------------------------------------------------------------------- /INSTALL.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/INSTALL.md -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/README.md -------------------------------------------------------------------------------- /blackbox/copy_lammps_results.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/blackbox/copy_lammps_results.sh -------------------------------------------------------------------------------- /blackbox/ibi.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/blackbox/ibi.sh -------------------------------------------------------------------------------- /blackbox/pmf.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/blackbox/pmf.sh -------------------------------------------------------------------------------- /blackbox/prepare_lammps_config.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/blackbox/prepare_lammps_config.sh -------------------------------------------------------------------------------- /blackbox/prepare_lammps_config_pmf.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/blackbox/prepare_lammps_config_pmf.sh -------------------------------------------------------------------------------- /config_files/bac_example/analysis_scripts/.keep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /config_files/bac_example/build/complex.crd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/bac_example/build/complex.crd -------------------------------------------------------------------------------- /config_files/bac_example/build/complex.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/bac_example/build/complex.pdb -------------------------------------------------------------------------------- /config_files/bac_example/build/complex.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/bac_example/build/complex.top -------------------------------------------------------------------------------- /config_files/bac_example/constraint/.keep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /config_files/bac_example/data/.keep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /config_files/bac_example/dcds/.keep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /config_files/bac_example/equilibration/.keep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /config_files/bac_example/fe-calc/amber_traj/.keep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /config_files/bac_example/fe-calc/build/com.crd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/bac_example/fe-calc/build/com.crd -------------------------------------------------------------------------------- /config_files/bac_example/fe-calc/build/com.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/bac_example/fe-calc/build/com.pdb -------------------------------------------------------------------------------- /config_files/bac_example/fe-calc/build/com.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/bac_example/fe-calc/build/com.top -------------------------------------------------------------------------------- /config_files/bac_example/fe-calc/build/lig.crd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/bac_example/fe-calc/build/lig.crd -------------------------------------------------------------------------------- /config_files/bac_example/fe-calc/build/lig.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/bac_example/fe-calc/build/lig.pdb -------------------------------------------------------------------------------- /config_files/bac_example/fe-calc/build/lig.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/bac_example/fe-calc/build/lig.top -------------------------------------------------------------------------------- /config_files/bac_example/fe-calc/build/rec.crd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/bac_example/fe-calc/build/rec.crd -------------------------------------------------------------------------------- /config_files/bac_example/fe-calc/build/rec.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/bac_example/fe-calc/build/rec.pdb -------------------------------------------------------------------------------- /config_files/bac_example/fe-calc/build/rec.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/bac_example/fe-calc/build/rec.top -------------------------------------------------------------------------------- /config_files/bac_example/mineq_confs/eq0.conf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/bac_example/mineq_confs/eq0.conf -------------------------------------------------------------------------------- /config_files/bac_example/mineq_confs/eq1.conf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/bac_example/mineq_confs/eq1.conf -------------------------------------------------------------------------------- /config_files/bac_example/mineq_confs/eq2.conf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/bac_example/mineq_confs/eq2.conf -------------------------------------------------------------------------------- /config_files/bac_example/run_scripts/.keep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /config_files/bac_example/sim_confs/sim1.conf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/bac_example/sim_confs/sim1.conf -------------------------------------------------------------------------------- /config_files/bac_example/simulation/.keep: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /config_files/ibi_example_poly1/angle.1.extrap.end: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/ibi_example_poly1/angle.1.extrap.end -------------------------------------------------------------------------------- /config_files/ibi_example_poly1/bond.3.new.1: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/ibi_example_poly1/bond.3.new.1 -------------------------------------------------------------------------------- /config_files/ibi_example_poly1/in.CG.lammps: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/ibi_example_poly1/in.CG.lammps -------------------------------------------------------------------------------- /config_files/ibi_example_poly1/interaction_list: -------------------------------------------------------------------------------- 1 | 1 1 2 | -------------------------------------------------------------------------------- /config_files/ibi_example_poly1/lammps_data_file: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/ibi_example_poly1/lammps_data_file -------------------------------------------------------------------------------- /config_files/ibi_example_poly1/pot.1.1: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/ibi_example_poly1/pot.1.1 -------------------------------------------------------------------------------- /config_files/ibi_example_poly1/pot.1.new.1.1: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/ibi_example_poly1/pot.1.new.1.1 -------------------------------------------------------------------------------- /config_files/ibi_example_poly1/rdf.1.1: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/ibi_example_poly1/rdf.1.1 -------------------------------------------------------------------------------- /config_files/lammps_lj_liquid/INFO: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/lammps_lj_liquid/INFO -------------------------------------------------------------------------------- /config_files/lammps_lj_liquid/in.CG.lammps: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/lammps_lj_liquid/in.CG.lammps -------------------------------------------------------------------------------- /config_files/namd_toy_model/build/leap.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/namd_toy_model/build/leap.log -------------------------------------------------------------------------------- /config_files/namd_toy_model/build/mol-solv.crd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/namd_toy_model/build/mol-solv.crd -------------------------------------------------------------------------------- /config_files/namd_toy_model/build/mol-solv.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/namd_toy_model/build/mol-solv.pdb -------------------------------------------------------------------------------- /config_files/namd_toy_model/build/mol-solv.top: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/namd_toy_model/build/mol-solv.top -------------------------------------------------------------------------------- /config_files/namd_toy_model/build/pep.pdb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/namd_toy_model/build/pep.pdb -------------------------------------------------------------------------------- /config_files/namd_toy_model/build/tleap.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/namd_toy_model/build/tleap.in -------------------------------------------------------------------------------- /config_files/namd_toy_model/build/tleap.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/namd_toy_model/build/tleap.log -------------------------------------------------------------------------------- /config_files/namd_toy_model/sim_confs/eq.conf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/namd_toy_model/sim_confs/eq.conf -------------------------------------------------------------------------------- /config_files/namd_toy_model/sim_confs/sim.conf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/config_files/namd_toy_model/sim_confs/sim.conf -------------------------------------------------------------------------------- /deploy/.jobscripts/test.sh: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /deploy/BioMD/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/BioMD/__init__.py -------------------------------------------------------------------------------- /deploy/BioMD/fabBioMD.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/BioMD/fabBioMD.py -------------------------------------------------------------------------------- /deploy/BioMD/templates/bac-archer: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/BioMD/templates/bac-archer -------------------------------------------------------------------------------- /deploy/BioMD/templates/bac-archer-nm-remote: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/BioMD/templates/bac-archer-nm-remote -------------------------------------------------------------------------------- /deploy/BioMD/templates/bac-archer-nmode: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/BioMD/templates/bac-archer-nmode -------------------------------------------------------------------------------- /deploy/BioMD/templates/bac-esmacs-whole-namd-supermuc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/BioMD/templates/bac-esmacs-whole-namd-supermuc -------------------------------------------------------------------------------- /deploy/BioMD/templates/bac-esmacs-whole-nmode-supermuc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/BioMD/templates/bac-esmacs-whole-nmode-supermuc -------------------------------------------------------------------------------- /deploy/BioMD/templates/bac-supermuc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/BioMD/templates/bac-supermuc -------------------------------------------------------------------------------- /deploy/BioMD/templates/bac-ties-archer: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/BioMD/templates/bac-ties-archer -------------------------------------------------------------------------------- /deploy/BioMD/templates/bac-ties-archer-v2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/BioMD/templates/bac-ties-archer-v2 -------------------------------------------------------------------------------- /deploy/BioMD/templates/bac-ties-supermuc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/BioMD/templates/bac-ties-supermuc -------------------------------------------------------------------------------- /deploy/BioMD/templates/bac-wonder-namd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/BioMD/templates/bac-wonder-namd -------------------------------------------------------------------------------- /deploy/BioMD/templates/bac-wonder1-nm-remote: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/BioMD/templates/bac-wonder1-nm-remote -------------------------------------------------------------------------------- /deploy/BioMD/templates/bac-wonder1-nmode: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/BioMD/templates/bac-wonder1-nmode -------------------------------------------------------------------------------- /deploy/BioMD/templates/bac-wonder1-nmode-test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/BioMD/templates/bac-wonder1-nmode-test -------------------------------------------------------------------------------- /deploy/BioMD/templates/bac-wonder2-nm-remote: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/BioMD/templates/bac-wonder2-nm-remote -------------------------------------------------------------------------------- /deploy/BioMD/templates/bac-wonder2-nmode: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/BioMD/templates/bac-wonder2-nmode -------------------------------------------------------------------------------- /deploy/BioMD/templates/bac-wonder2-nmode-test: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/BioMD/templates/bac-wonder2-nmode-test -------------------------------------------------------------------------------- /deploy/BioMD/templates/fep.tcl: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/BioMD/templates/fep.tcl -------------------------------------------------------------------------------- /deploy/BioMD/templates/namd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/BioMD/templates/namd -------------------------------------------------------------------------------- /deploy/BioMD/templates/nmode.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/BioMD/templates/nmode.in -------------------------------------------------------------------------------- /deploy/NanoMD/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/NanoMD/__init__.py -------------------------------------------------------------------------------- /deploy/NanoMD/fabNanoMD.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/NanoMD/fabNanoMD.py -------------------------------------------------------------------------------- /deploy/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/__init__.py -------------------------------------------------------------------------------- /deploy/data_proc/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/data_proc/__init__.py -------------------------------------------------------------------------------- /deploy/data_proc/data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/data_proc/data.py -------------------------------------------------------------------------------- /deploy/data_proc/dataNanoMD.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/data_proc/dataNanoMD.py -------------------------------------------------------------------------------- /deploy/fab.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/fab.py -------------------------------------------------------------------------------- /deploy/lammps-systems.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/lammps-systems.yml -------------------------------------------------------------------------------- /deploy/machines.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/machines.py -------------------------------------------------------------------------------- /deploy/machines.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/machines.yml -------------------------------------------------------------------------------- /deploy/machines_user_example.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/machines_user_example.yml -------------------------------------------------------------------------------- /deploy/templates.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/templates.py -------------------------------------------------------------------------------- /deploy/templates/lammps: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/templates/lammps -------------------------------------------------------------------------------- /deploy/templates/ll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/templates/ll -------------------------------------------------------------------------------- /deploy/templates/ll-supermuc: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/templates/ll-supermuc -------------------------------------------------------------------------------- /deploy/templates/lsf1: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/templates/lsf1 -------------------------------------------------------------------------------- /deploy/templates/lsf2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/templates/lsf2 -------------------------------------------------------------------------------- /deploy/templates/no_batch: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/templates/no_batch -------------------------------------------------------------------------------- /deploy/templates/pbs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/templates/pbs -------------------------------------------------------------------------------- /deploy/templates/pbs-archer: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/templates/pbs-archer -------------------------------------------------------------------------------- /deploy/templates/redis_header.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/templates/redis_header.txt -------------------------------------------------------------------------------- /deploy/templates/sge: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/deploy/templates/sge -------------------------------------------------------------------------------- /deploy/test_data/test_plot.txt: -------------------------------------------------------------------------------- 1 | 1 1 2 | 2 2.2 3 | 4 3.9 4 | 8 7.2 5 | 16 13.1 6 | -------------------------------------------------------------------------------- /doc/FabBioMD-examples.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/doc/FabBioMD-examples.md -------------------------------------------------------------------------------- /doc/FabNanoMD-examples.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/doc/FabNanoMD-examples.md -------------------------------------------------------------------------------- /doc/commands-list.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/doc/commands-list.txt -------------------------------------------------------------------------------- /fabfile.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/fabfile.py -------------------------------------------------------------------------------- /python/IBI.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/python/IBI.py -------------------------------------------------------------------------------- /python/IBI.py.requirements: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/python/IBI.py.requirements -------------------------------------------------------------------------------- /python/PMF.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/python/PMF.py -------------------------------------------------------------------------------- /python/filter_pot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/python/filter_pot.py -------------------------------------------------------------------------------- /python/lib/.hgignore: -------------------------------------------------------------------------------- 1 | LammpsIO.pyc 2 | -------------------------------------------------------------------------------- /python/lib/DataAnalysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/python/lib/DataAnalysis.py -------------------------------------------------------------------------------- /python/lib/DataMorphing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/python/lib/DataMorphing.py -------------------------------------------------------------------------------- /python/lib/LammpsIO.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/python/lib/LammpsIO.py -------------------------------------------------------------------------------- /python/lib/LammpsOutputAnalysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/python/lib/LammpsOutputAnalysis.py -------------------------------------------------------------------------------- /python/lib/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /python/plot_lammps.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/UCL-CCS/FabSim/HEAD/python/plot_lammps.py --------------------------------------------------------------------------------